Friday, March 25, 2011

Off to another meeting so don't have time to write up details of the JGI User Meeting that just ended. But I am posting my tweets and some related tweets here. Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the road ...

Wednesday, March 23, 2011

Well, my snarky blog style with some of my awards comes with some risks. Today I experienced one of them. Stephan Schuster gave me some serious major grief over a post I wrote a few years ago. In the post I gave him an award for "Worst new omics word" for the word museomics. I gave this award because, well, I don't like the word. I stand by my complaints about the word. But Stephan did highlight ( in his comments to me in the back of the room at the JGI User Meeting) that the word has been remarkably useful at getting money and attention for museum based genomics studies.

Friday, March 18, 2011

This is a post about a paper that has been a long long time coming. Today, a paper of mine is being published in PLoS One. The paper is titled "Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees" and is available at http://dx.plos.org/10.1371/journal.pone.0018011. (or if that link does not work you can get a copy here). This paper represents something I started a long time ago and I am going to try to describe the story behind the paper here.

I note - we are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release. But this will be a bit longer than most press releases. I note - my key fear here is that somehow in my communications with the press or in our text in the paper or in this post I will overstate our findings. Here is the punchline - we found some very phylogenetically novel forms of phylogenetic marker genes in metagenomic data. We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. The They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.

I found out a few days ago and am rearranging some things to go to Boston April 13 for the award ceremony at the Bio-IT World Conference and Expo.

From the Bioinformatics Organization web site:

Benjamin Franklin (1706-1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, he freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of the Bioinformatics Organization, Inc. that he embodied the best traits of a scientist, and we seek to honor those who share these virtues

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

Tuesday, March 08, 2011

A wee bit late but thought I would give an update on a recent trip. In January I went on a little trip to Southern California. The trip started with a simple plan - Susan Golden invited me to give a talk at UCSD. After my usual complications in planning, I finally agreed to a date (1/19) after finding out the Phil Bourne, Editor in Chief of PLoS Computational Biology was helping organize a meeting starting 1/19 entitled "Beyond the PDF" to discuss the future of scientific publishing. So this seemed like a perfect mix. Go down to UCSD for one thing and stay for another. Short flight and easy to change. Seemed ideal

Of course I had to make it more complex so I contacted some friends at the J. Craig Venter Institute to see if they would be around and unfortunately my friend Jeff Hoffman was not going to be around. But he connected me to Craig Venter and his wife Heather Kowalski and though what I really wanted was to just see if they would be around for a visit or dinner - I ended up getting roped into giving a talk there on the 18th.

Monday, March 07, 2011

Well, I realize of course some things take time, but I cannot imagine it is that hard to restore free access to all papers reporting genome sequence data. Nature had promised to do this when many papers were published but recently I noticed that this was not being done. For some background see:

Friday, March 04, 2011

Well, in case you did not see, yesterday I got really pissed off at Nature Publishing Group. Short summary - many articles of mine that were supposed to be freely available on their journal sites were not. For more information see

People from Nature Publishing Group have responded quite quickly saying they will look into this and try to fix it and indeed they have fixed many if not all of the mistakes in accessibility I found yesterday. Glad they responded so quickly. However, their response raises quite a few questions. Like "what happened?" - as in - why did access get closed off? And why were they charging to for article use when they should not have been?

It would be good for Nature to publish / post a full description of what went wrong. And perhaps they will. Apparently, it was just a glitch in the system. Whatever the cause however, almost certainly some people paid for access for articles that were supposed to be freely available. I am calling on Nature here to audit their systems and return all money that was paid for such access.

Thursday, March 03, 2011

Yuck. Am getting really pissed off right now. It is 1:30 AM. I am tired. And I am now angry. I was writing a post about a recent trip, and wanted to link to an article I was a coauthor on. The article was the paper on sequencing and analysis of the genome of Arabidopsis thaliana. So I googled "Arabidopsis Genome Initiative" and found the link to the paper at Nature. And much to my surprise I found this waiting for me:

Why is that a surprise? Because the genome paper is supposed to be freely available to all forever, under a policy Nature developed for papers reporting new genome sequence data. I am tired or I would write more about the history of this. But another time.

So then I looked for other genome papers I have published in Nature. And so I looked for the Plasmodium genome paper. And I got this:

Grand. That one was supposed to be free forever too.

And so I looked at many others. And for most, I got the same thing. Not freely available. If I were not at home, I would not have noticed this because I have access at work. And I could get access at home by setting up the UC Davis library VPN system. But fortunately I do not do that or I would not have discovered that Nature, not for the first time mind you, has turned articles that were supposed to be freely available forever into charge for access articles. I know. I know. This is probably just some glitch in their system. They really do seem committed to trying to make these available. But clearly, the system either does not work well. Or they are not committed to it. Either way this is really annoying. In some cases, the papers were sold to communities of scientists in part with the "These will be freely available to all forever" line as part of the sell. I am deeply worried about my recent Genomic Encyclopedia paper which is also supposed to be freely available forever. Right now it still is, which is good. But how long will that last? And I note, though Nature people have said they would try and fix it, Nature still incorrectly claims Copyright to that article on the PDF. Personally, I like most of the people I know at Nature Publishing Group and like many of the things NPG does. But this is getting really annoying. And it just goes to show - the ONLY way to go it seems is full, complete Open Access which the journals cannot magically then take away.

Tuesday, March 01, 2011

Norman R. Pace, from UC Boulder, gave a talk at UC Davis last week about microbial diversity. In his talk he discussed some of his recent Sloan Foundation funded work on “microbiology of the built environment” including studies of shower heads, indoor swimming pools, water supplies, and hospitals.

Pace is one of the pioneers of DNA based studies of microbes in the environment. His initial work on studies of ribosomal RNA from uncultured organisms (started more than 20 years ago) helped launch the field. For more information on his work see his lab page here

If you are interested in the microbes that are found in showerheads, his PNAS paper on this (which can be found here) on this from 2 years ago got a lot of press. See for example this Science Friday
and this New York Times article by Nicholas Wade.

I note we have a new project as part of this Sloan program to facilitate communication and networking and sharing information as part of this project. My lab is creating something called "microBEnet" - the microbiology of the built environment network. We are just getting our real site up and running. For now you can find out some information at a temporary page http://microbenet.blogspot.com/